Wednesday, May 25, 2016

The Naked Ape: An Open Letter to BioLogos on the Genetic Evidence

Toward a Consensus

Dennis Venema, professor of biology at Trinity Western University, has written a series of articles that have been noted by evolutionists for their clarity and persuasiveness. So as a collector of evidences and reasons why evolution is a fact, I was interested to see Venema’s articles. What does the professor have to say to help confirm what Samuel Wilberforce rhetorically called “a somewhat startling conclusion”?

One of Venema’s basic points (see here and here) is that the genomes of different species are what we would expect if they evolved. Allied species have similar genomes, and genetic features fall into evolution’s common descent pattern:

If indeed speciation events produced Species A – D from a common ancestral population, we would expect their genomes to exhibit certain features when compared to each other. First and foremost, their overall genome sequence and structure should be highly similar to each other – they should be versions of the same book, with chapters and paragraphs of shared text in the same order. Secondly, the differences between them would be expected to fall into a pattern.

Does the evidence confirm these evolutionary expectations? Venema answers with an emphatic “yes.”

Here Venema is appealing to the empirical evidence. He is comparing the evidence to the theory of evolution, and finding that the evidence confirms evolution’s predictions. This means the theory can be empirically evaluated. And if evolution can be genuinely evaluated empirically, then it is, at least theoretically, possible for evolution to fail. If the evidence can confirm evolution, then it also can disconfirm evolution.

This is important because focusing the attention on the evidence means the non scientific arguments go away and science is allowed to speak. What does it say? Here I will take the opposing view, for it seems that what the science shows is that Venema’s claim, that the genetic evidence confirms evolutionary predictions, is inaccurate.

This is not to say that evolutionary explanations cannot be offered. As philosophers well understand, another sub hypothesis is always possible. Such hypotheses raise more profound questions of parsimony, likelihood and so forth. But it seems that such philosophical questions ought to be addressed after there is a consensus on what the empirical evidence has to say. The goal here is to move toward that consensus. Venema, and evolutionists in general, make a straightforward claim about the evidence. We ought to be able to dispassionately evaluate that claim.

Of course I realize that reaching consensus is not as simple as reading an article. There will be differing interpretations by fair-minded critics. And the topic of origins is certainly not always dispassionate. If you argue against evolution you will be disparaged. My response to such attacks has and always will be to forgive.

One final preliminary is simply to point out that it is a challenge just to do justice to this story. A thorough treatment could easily require an entire volume. But a few, typical, examples will have to suffice. They can provide readers with an approximate understanding how the evidence bears on Venema’s claim.

What does the evidence say?

For starters, phylogenetic incongruence is rampant in evolutionary studies. Genetic sequence data do not fall into the expected evolutionary pattern. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many.

MicroRNAs are short RNA molecules that regulate gene expression, for example, by binding to messenger RNA molecules which otherwise would code for a protein at a ribosome. Increasingly MicroRNAs are understood to be lineage-specific, appearing in a few species, or even in just a single species, and are nowhere else to be found. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional [evolutionary] tree.” It is, another evolutionist admitted, “a very serious incongruence.”

Trichodesmium or “sea sawdust,” a genus of oceanic bacteria described by Captain Cook in the eighteenth century and so prolific it can be seen from space, has a unique, lineage-specific genome. Less than two-thirds of the genome of this crucial ammonium-producing bacteria codes for proteins. No other such bacteria has such a low value, and conversely such a large percentage of the genome that is non coding. This lineage-specific genome, as one report explains, “defies common evolutionary dogma.”

It is not unusual for similar species to have significant differences in their genome. These results have surprised evolutionists and there does not seem to be any let up as new genomes are deciphered.

The mouse and rat genomes are far more different than expected. Before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome. As one paper explained:

Before the launch of the Rat Genome Sequencing Project (RGSP), there was much debate about the overall value of the rat genome sequence and its contribution to the utility of the rat as a model organism. The debate was fuelled by the naive belief that the rat and mouse were so similar morphologically and evolutionarily that the rat sequence would be redundant.

The prediction that the mouse and rat genomes would be highly similar made sense according to evolution. But it was dramatically wrong.

One phylogenetic study attempted to compute the evolutionary tree relating a couple dozen yeast species using 1,070 genes. The tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches. It was “a bit shocking” for evolutionists, as one explained: “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 yeast.”

What is interesting is how this false prediction was accommodated. The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene.

These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.”

And how do we know that these genes have strong phylogenetic signal. Because they gave the right answer. This raises the general problem of prefiltering of data. Prefiltering is often thought of merely as cleaning up the data. But prefiltering is more than that, for built-in to the prefiltering steps is the theory of evolution. Prefiltering massages the data to favor the theory. The data are, as philosophers explain, theory-laden.

But even prefiltering cannot always help the theory. For even cleansed data routinely lead to evolutionary trees that are incongruent (the opposite of consilience). As one study explained, the problem is so confusing that results “can lead to high confidence in incorrect hypotheses.” As one paper explained, data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence. And although evolutionists thought that more data would solve their problems, the opposite has occurred. With the ever increasing volumes of data (particularly molecular data), incongruence between trees “has become pervasive.”

What is needed now is less data. Specifically, less contradictory data. As one evolutionist explained, “if you take just the strongly supported genes, then you recover the correct tree.” And what are “strongly supported” genes? Those would be genes that cooperate with the theory. So now in addition to prefiltering we have postfiltering.

Another issue are the striking similarities in otherwise distant species. This so-called convergence is rampant in biology and it takes on several forms.

Consider a paper from the Royal Society on “The mystery of extreme non-coding conservation” that has been found across many genomes. As the paper explains, there is currently “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Here is how the paper summarizes these findings of extreme sequence conservation:

… despite 10 years of research, there has been virtually no progress towards answering the question of the origin of these patterns of extreme conservation. A number of hypotheses have been proposed, but most rely on modes of DNA : protein interactions that have never been observed and seem dubious at best. As a consequence, not only do we still lack a plausible mechanism for the conservation of CNEs—we lack even plausible speculations.

And these repeated designs, in otherwise different species, are rampant in biology. It is not merely a rare occurrence which perhaps evolution could explain as an outlier. That the species do not fall into an evolutionary tree pattern is well established by science.

Furthermore, these repeated designs do not merely occur twice, in two distant species. They often occur repeatedly in a variety of otherwise distant species. So now the evolutionist must not only believe that there are many of these repeating design events, but that in most cases, they repeat multiple times, in disparate species.

Evolutionists have labeled this evidence as recurrent evolution. As a recent paper explains:

The recent explosion of genome sequences from all major phylogenetic groups has unveiled an unexpected wealth of cases of recurrent evolution of strikingly similar genomic features in different lineages.

In addition, many instances of a third more puzzling phylogenetic pattern have been observed: traits whose distribution is “scattered” across the evolutionary tree, indicating repeated independent evolution of similar genomic features in different lineages.

Of course these puzzling, striking similarities cannot be explained by common evolutionary history. Instead, they are explained by common evolutionary forces:

As ancestrally shared features are the result of a common evolutionary history, shared features evolved by recurrent evolution are often the result of common evolutionary forces acting on different lineages.

If the pattern fits the evolutionary tree, then it is explained as common evolutionary history. If not, then it is explained as common evolutionary forces.

With all of this contradictory evidence, even evolutionists have realized in recent years that the traditional evolutionary tree model is failing. As one evolutionist explained, “The tree of life is being politely buried.”

There are many more fascinating examples of biological patterns that are not consistent with the expected evolutionary pattern. These are not anomalies or rare exceptions. Here we have focused on the genetic level since that was the theme of Venema’s article. It seems that the species and their genomes do not fall into a consistent evolutionary pattern as evolutionists such as Venema claim. This does not mean evolutionists cannot explain any of this. They have a wide spectrum of mechanisms to draw upon, of varying levels of speculation and likelihood. These explanatory mechanisms greatly increase the theory’s complexity. They raise questions of realism, and whether the theory is following the data, or the data is following the theory. But such questions are for another day.

The point here is that evolutionist’s claims that the genomic data broadly and consistently fall into the evolutionary pattern and expectations do not seem to reflect the empirical data. This is the first step in moving the discourse forward. We need to reach consensus on what the evidence reveals.

Next time I will continue with an examination of the next evidences Venema presents.

[Ed: Comments critical of any position are welcome below, but they should be in a constructive tone]

CorneliusThanks you for the very interesting article. I think you are surfacing a very important debate especially because there is not consensus in the ID community. Do we have common biochemistry or common decent?

Most, I believe including Dr. Hunter, assume the earth to be about 4.5 billion years old, and that life extends back at lease 3.5 billion years.

Is that true Cornelius? Do you accept the scientific fact of a 4.5 billion year old Earth and life being present for at least the last 3.5 billion years?

I'm pretty sure there's nobody here with any different opinion

Then which is correct? 4.5 billion and 6000 can't both be right. What does ID say? It makes a huge difference in how ID attempts to explain what we empirically observe in the fossil and genetic records.

Why is this such a problem for you? Do you really have a problem with who believes what about the age of the earth, or is it that anyone should believe that God created it in the first place?

Surely you know that once God is granted first position as creator everything else becomes subject to His design and purpose. The age of the earth becomes something of an intellectual pursuit without real consequence (for most people).

If Biologos has happened upon the correct creation scenario, and God did in fact create through evolution, doesn't that still allow the view that evolution is at best implausible as an unguided natural process?

Dr. Hunter was the first author I'd encountered that made me really look at what evolutionary theory offered. There is reason to consider evolutionary theory, I get it. I also get that when you start to study the nuts-n-bolts of it there doesn't seem to be any rational explanation for how evolution could be possible as an unguided natural process.

You seem to want to argue against faith in God and do so with an argument against YEC (not an argument per se, more of a diatribe). Is that really an argument against God? For some there is no contradiction to say God created light in transit. Others easily adopt an OEC point of view, which completely circumvents your favorite complaint against creationists.

So what is it exactly that keeps you commenting on each and every article posted here? Each time with the same basic bent: Cornelius Hunter is a crazy YEC fanatic and nothing he says should be given a moments consideration.

Why is evolution so sacred to you? Why is it essential that kids learn it and believe it? How has evolution every really helped science?

Seems to me evolutionary theory is completely unnecessary when it comes to understanding what is, only the "science of evolution" benefits from grants to study evolution. We can examine genetic code and accept what we find without even worrying about common descent. Since common descent fails so often, which is the point of the OP, it would seem research would be better off without it. So why is wrong to adhere to ID or creationism? Do you hate God? Are you a walking trailer for God's Not Dead?

You are one of the most prolific commenters on this blog, yet I can't recall a single comment by you that I would classify as productive. I've not read all your comments by any measure, but the sample I have read leaves you sounding as one with an axe to grind on a personal level against God.

So what is it exactly that keeps you commenting on each and every article posted here?

Simple. My country's future depends in large part on the scientific understanding and abilities of our population. The dissemination of anti-science propaganda in the name of pushing religion is antithetical to those needs.

Your underlying assumption seems to be if I believe in YEC or God then I can't contribute to the future. Tell that to the many great minds of science in the past that were believers. And though they are probably in the minority there are also many current scientists that are believers.

So those who believe in a YEC or God can't contribute to the country's future? You might want to look at the beliefs of some of the most famous scientists in the past. Also though I'm sure in the minority there are still a lot of current scientists who are believers. And in the fields I know more aerospace and engineering the number of believers that I speak to regularly is even higher. But I guess none of them contribute much to the future.

Your underlying assumption seems to be if I believe in YEC or God then I can't contribute to the future

Completely false. My beef is with those who attack and belittle science and scientists in order to push their religious agenda. That's ALL this blog does. I push back at those who would lower science standards and allow anti-science YEC nonsense back into public school science classrooms. This sort of nefarious action undercuts the public's ability to understand technical scientific issues. Then we get a scientifically illiterate population of AGW deniers, anti-vaxxers, people believing in homeopathy and all sorts of woo.

Believe in whatever God or Gods you choose, practice any religion you want. I'll support you right to do so 100%. Just stop attacking honest scientists and keep your religion out of the science.

What you claim is rubbish and everyone knows it. Only anti-God zealots would make such a claim as you did. Zealotry is personal so only you can know why you do it, but you are in no way promoting our nation's future by attacking YEC or God.

If you're really concerned with the future of the nation, or humanity for that matter, you would do better to become religious. It's known that religious belief stabilizes society while atheism produces apathy and despondency, particularly in youth. While teaching God in schools may appear to be the goal of Christians, it really isn’t. But science class has become scientism class. Do you even know why that's bad?

If you really value the future of the nation then do something truly productive with your time. Kids are being raised by schools instead of parents. Schools aren’t allowed to teach morality, they can’t even teach the difference between boys and girls anymore as it relates to which locker room to use. Why wouldn’t a teen choose a life of drugs when there is no right or wrong they can rely on? Act like an idiot and the state gives you drugs, which they either take or sell.

Your ignorance extends to kids.

GR, you have been completely befuddled by your own anti-God zealotry. Kids need hope and purpose; I, among many others, know that hope and purpose exist. It may not be the job of science to teach hope and purpose, but your brand of science would rob kids of them. How? Through your labeling and institutionally supported bigotry. Why? because it’s true? No, that is easily disputed. The only reason is to destroy any competing worldview. Does this help students? Of course not, it makes you feel better about your own belief system.

The human need for purpose is so great that even atheists like you, who believe that the entire universe will one day be cold and lifeless, take on campaigns like “saving the future of science from nutjob Christians” (paraphrased). You invent your own purpose which, curiously, revolves around derailing the sense of purpose held by others far more than actually pursuing the science you purport to defend.

All this because why again? Oh yea, to save the doomed world from AGW deniers, anti-vaxxers, and people believing in homeopathy. Obviously the only serious threat to kids when contrasted with minor nuisances of drug addiction, family breakdown, welfare dependency, and social apathy. “The scientific understanding and abilities of our population” isn’t dependent on kids learning how to read, manage a checkbook, or to discern the value of the family unit. It’s all about faith in AGW and ToE.

You really need to admit this campaign of yours has nothing to do with “the future of the nation”. Kids who can’t read aren’t going to express great scientific understanding. A generation on Prozac isn’t likely to produce the next Einstein. You aren’t saving anything, you’re defending your own biases. You do nothing but rail against the idea that you could be wrong, and God just might be your judge one day.

Sorry ohandy1 but the only person off his rocker is you. You Fundies so desperately need to be the poor persecuted VICTIM all the time you see everything as attacking your God. Your paranoia is off the charts.

Wanting to preserve the integrity of science education in the country has nothing, NOTHING to do with any attacks on your personal religious beliefs. It just so happens a few of your religiously motivate Fundie buddies are trying to force their anti-science nonsense back into public schools. They are the root cause of any conflict, not anyone trying to stifle your personal religious beliefs.

Cornelius Hunter:"Yes, I'm not a young-Earther. I don't view that as relevant to the origins discourse."

Yes, I agree. Time is irrelevant. While I do not believe that many of these huge numbers offer any accurate certainty, I have no problem if all the materials which make up Earth and the entire universe have been here to billions upon billions of years. So what ? I don't think science can accurately come up with exact timing of events, but more accurately it can tell us when things did not occur. For example is is clear and has been for decades that the Universe and all life didn't just happen in a little over 6000+ years.

Cornelius Hunter:"IOW, age is not the problem with evolutionary theory."

Ghostrider, I guess you would call me ignorant, but you don't have to except all of what popular science claims to be truth. As in the fields of engineerimg, aerospace, computers, etc... what difference does your belief in YEC or God make. You seems to insinuate that you must accept all of the conclusions of the current scintific pardagrim. I can tell you that many in those fields do believe in YEC and God and I would put their achievement or contributions up against nearly every atheist I have ever met.

As in the fields of engineerimg, aerospace, computers, etc... what difference does your belief in YEC or God make.

You didn't read a single word I wrote, did you? No one said your can't have YEC beliefs and not do science. What I said was I fight against teaching those YEC beliefs AS science in public schools. What would you do if a group of nutters started demanding aerospace schools stop teaching Bernoulli's principle, that airflow over aircraft wings causes lift and instead taught lift was caused by God's Little Angels holding the plane off the ground. Would you want your family to board a plane designed by someone with that "knowledge"?

That's exactly what the YEC nutters are demanding we do to science education in the biological sciences. Dump 150+ years of verified results and replace it with their fantasy religious ID-Creationist woo.

You’re NOT protecting the integrity of science. That’s my point. You make science out to be a victim of assault by religion in need of your defense.

I’m paranoid?

As I read this blog I read evaluations of, in large part, peer reviewed science papers. When these papers include non-scientific claims like “because it evolved that way” they are pointed out. This isn’t anti-science, it’s very much PRO-science. It reads to me as “get your religious faith out and stick to the science – if you don’t know just say so”. And in reply to each such article is a comment from you calling Cornelius a liar and worse. As though you personally have been attacked.

Besides, how does YEC for a moment make science less capable of finding the cure to cancer or getting someone on Mars. What about OEC? Is that anti-science? I’ve read papers describing the errors of Einstein’s theories, also anti-science? An article on phy.org claims the big bang never happened (not Christians by the way), are they anti-science?

Sounds like anyone who would challenge what you believe is anti-science, yet you accuse me of crying victim. Should science only work within truth as defined by consensus? Do you even know what science is? (yea I said it. What is science in your world if it cannot be challenged?)

Teaching evolution as RMNS doesn’t persecute religion, it damages science by promoting one. But as I said, your zealotry is personal to you.

If you really wanted to defend ToE (more accurately - your worldview) you could answer some of the finer points in this OP, for example the study of yeast species. How has Cornelius misrepresented or misunderstood this study? Without calling him a liar, can you explain why his objection to the accommodation is invalid? What is wrong with his conclusions?

Even still, if you fail to defend ToE, science will remain just fine. Christianity nor creationism can threaten science, only your beliefs.

Thanks for the interesting article. I have placed it in my "source" folder because it has so many good source links in it. My current position is very strongly ID, but also holds to common descent. You make a good case to reconsider common descent. (Still can't get past the disease producing point mutations shared by chimp and human, however.)

I would love to see other biologists respond with their interpretation of your source links.

BTW, my alma mater is TWU. As you know, but the other readers may not, it is a fairly radically Christian institution. I am quite surprised that one of their professors would make such a presentation.

ID has no explanation for any natural phenomenon. It has no mechanism, no timeline, no details of any sort. Saying "The Designer did it!" merely replaced "GOD did it" to circumvent laws prohibiting the government favoring religion in science classrooms.

GhostriderSimple. My country's future depends in large part on the scientific understanding and abilities of our population. The dissemination of anti-science propaganda in the name of pushing religion is antithetical to those needs."

LukasID does not claim that evolution is false. It claims that some things we observe in nature are best explained by design and not processes that we observe in nature. Small changes like the paper you cited are certainly expected by natural variation if it can be accomplished by a few mutations. Since the genome is a sequence like your cell phone or the any latin or germanic language its function will begin to break down with more than a few random changes. If you were to make a few random changes to your direct dial numbers you would still have a good set of stored numbers but if you made several hundred then your direct dial feature on your cell phone would certainly be almost useless.

There was a period of rapid evolution in bats, which makes determining the phylogeny more difficult. However, the paper you cite actually explain many of the incongruences as being due to saturation, as well as lineage soring.

Cornelius Hunter: In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional [evolutionary] tree.”

Dolgin's trees are based on microRNA, but "highly heterogeneous rates of microRNA gain and loss, pervasive secondary loss, and sampling error collectively render microRNA-based inference of phylogeny difficult." See Thomson et al., A critical appraisal of the use of microRNA data in phylogenetics, PNAS 2014.

Cornelius Hunter: As one evolutionist explained, “The tree of life is being politely buried.”

So we don't get conflicting signals, except when we do. And there is one main tree, except where there isn't. It's beginning to look like organisms really resemble designed things. Designed things can be arraigned into a nested hierarchy. it's just that artifacts have mixing and matching of traits. Well, it seems that organisms also have lots of mixing and matching.

Thanks for your reply. All good points, but this is what the OP meant. Evolutionary explanations can always be offered. There is always some way to explain the data according to evolution. But such explanations are needed because the evidence does not strongly support evolution. We can examine each case, and discourse on the likelihood of each explanation. But we first need to have consensus on what the evidence says, and how it bears on the theory.

Lukas"So if I got your answer right that new species can arise thanks to evolution but the "building blocks" of life were design. Am I correct?"Yes this is true but only if species are almost genetically identical. When the changes get larger the sequential space of the genome becomes a large obstacle.I am somewhat neutral on the ID movement. I think when you restrict it to its explanation based on scientific inference it is limited because like darwinian evolution there is no testable mechanism that tells you how one kind becomes another. ID in its purest sense is only inferring design was requited for the genetic changes which are highly specified genomic sequences. ID does not answer the how question of change. When I have done cancer research it is useful to think of the cell as designed because it does follow human design rules of process control and redundancy. If you identify one protein that is controlled by a destruction mechanism the chances are good a new similar protein will follow the same rules.

"For instance, which two of these three are most objectively similar: cat, dog, sponge?"

Sure,a cat ismore similar to a dog. But you are saying "more similar than" not similar. How much similarity between a cat and a dog support "evolution"? How much similar ToE predicts between dog and cat?Why?

Thanks for the answer. So if I got it right it means in ID that a new specie can arise but it will be only limited to its family for example a new specie wasp can arise thanks to evolution and natural pressure but it will be only a new wasp specie and nothing more. It cannot evolve further into something more complex. Did I get it right how the people in ID are looking at it?

LukasI think you basically have it. ID does not put hard mathematical limits but says that a new genome sequence infers that design was involved. The inference comes from knowing that humans can design sequences like languages. There is no direct evidence that original sequences can be originate be produced without design.

No, what is objective is that the cat is more similar to a dog than a sponge. I were saying that similarity between a cat and a dog human and monkey is not scientific because you have no reference. How much similarity is similar. You have to add compared with somethng (the sponge) then you have a reference.

Blas: How much similarity between a cat and a dog support "evolution"?

Zachriel: It's not mere similarity, but the nested hierarchy, which supports branching descent.

Well then it is not similarity the evidence but the nested hierarchy.

Zachriel: Well, we have an imperfect nested hierarchy.

And then you have again a problem how much imperfections in the nested hierarchy still support ToE? There is an objective parameter to say this imperfection is predicted by ToE more than that isn´t?

Another excellent post, Cornelius. Don't expect much from Darwinists in terms of a logical, reasoned response. I learned a long time ago that the vast majority of Darwinists are hopelessly deluded and willfully blind to the truth. Their loss...not mine (or yours).

Thanks a lot for explaining it to me. I was only interested if both "looks" can produce new animal species now I know they can. I got it cleared out in evolution but I did not know how was the ID look at it. Thanks a lot for your patience and replies in a polite manner.

The consilience of the evidence strongly supports common descent, and many of the conflicts to the nested hierarchy are evidence of specific and testable mechanisms, such as natural selection.

This claim illustrates the problem that the OP is trying to resolve. If empirical contradictions are simply transformed into virtues, then there is no hope for informed, meaningful discourse. If we continue with these claims that are not vulnerable to the empirical data, then evolution has no empirical content and the discussion simply is incommensurate, as philosophers put it.

What we are trying to establish here is a reasoned, intelligent discourse. The prerequisite is a common understanding of the scientific evidence.

Zachriel said:The consilience of the evidence strongly supports common descent, and many of the conflicts to the nested hierarchy are evidence of specific and testable mechanisms, such as natural selection.

That is not a scientific claim and do not answer tobthe question how much imperfections in the nested hierarchy still support ToE? Consilience and acutal testable mechanisms are not strong evidence for common descent are just possible explanations for the imperfections of the nested hierarchy.

Cornelius Hunter: If empirical contradictions are simply transformed into virtues, then there is no hope for informed, meaningful discourse.

They're not "empirical contradictions", but rather countervailing influences. Branching descent leads to a nested hierarchy, while natural selection sometimes confounds the nested hierarchy. Other mechanisms also counter the pattern expected of branching descent, including hybridization, saturation, and horizontal gene transfer.

Natural selection means that certain trait will appear in distantly related organisms; for instance, both a fish and a dolphin have hydrodynamic shapes. This is due, not to their shared common ancestry, but to selection for life in the water. Another example is prestin, which is a protein involved in high-frequency hearing. While prestin is largely conserved in mammals, and synonymous substitutions support the standard phylogeny, non-synonymous substitutions in whales and bats show a closer relationship than would otherwise be expected.

Then you are explaining part of the imperfections by saying that a blind ramdom process found the same solutions for the same problems. An intelligent mind can also do that. Why this explanation would support common descent?This NS it is not testable. We do not observe actual mutations mutations of the prestin that led actual mammals to achieve high frequency hearing.

Zachriel said The nested hierarchy and fossil succession support common descent.

A perfect nested hierarchy would be a strong support to common descent, as Darwin knew the nested hierarchy is not perfect proposed that an imperfect nested hierarchy would still support CD. The point is how much imperfections still support CD? There is any objective measure of the imperfections of the nested hirarchy that establish there is still support for CD?As everybody agrees the fossil record is incomplete it cannot be strong support for nothing.

Zachriel said What we observe is that synonymous substitutions support the standard phylogeny, while the non-synonymous substitutions support adaptation to similar situations. The concept of “susbstitutions” is a derivation of ToE, then it cannot be support of ToE is circular reasoning.

Blas: A perfect nested hierarchy would be a strong support to common descent, as Darwin knew the nested hierarchy is not perfect proposed that an imperfect nested hierarchy would still support CD.

He proposed specific and testable mechanisms to explain the variations of the basic pattern, including natural selection and hybridization.

Blas: There is any objective measure of the imperfections of the nested hirarchy that establish there is still support for CD?

Is the Earth's orbit a perfect ellipse?

Blas: The concept of “susbstitutions” is a derivation of ToE, then it cannot be support of ToE is circular reasoning.

Gee whiz, Blas. We can define substitutions without reference to theory. Call them "differences" if it makes you feel better. Synonymous difference support the standard phylogeny. Non-synonymous differences support natural selection.

Zachriel said:He proposed specific and testable mechanisms to explain the variations of the basic pattern, including natural selection and hybridization.

The natural selection testable is the one that eliminates the less reproductive members of a population. If you want to test NS as the mechanism by why dolphin and a fish are similar you need to test the selection of a Labrador with “fishy” traits. hybridization is a possible explanation for some of the imperfections, but a posible explanation do not give strong support.

Zachriel said:Is the Earth's orbit a perfect ellipse?

No. And?

Zachriel said:Gee whiz, Blas. We can define substitutions without reference to theory. Call them "differences" if it makes you feel better. Synonymous difference support the standard phylogeny. Non-synonymous differences support natural selection.

Synonymous differences fit the nested hierarchy expected from the standard phylogeny. Non-synonymous differences support the standard phylogeny, except when the organisms are under selection for high-frequency hearing.

Zachriel said: That's right. When combined with sources of variation, it can lead to adaptive change, such as is observed with Darwin's finches. .

Yes, we observe adaptive changes, not evolutive change.

Zachriel said: That's right. There are multiple influences on the orbit of a planet, so we don't expect perfect ellipses. Instead, we have complex, and possibly chaotic, orbits.

And so? It is almost impossible to calculate the gravitational resultants of three bodies imagine a star system. The support of the theory of gravity do ot come from the explanations of the difference between the actual orbits and the ellipses but from the scientific experiments of gravity.

Zachriel said: Synonymous differences fit the nested hierarchy expected from the standard phylogeny. Non-synonymous differences support the standard phylogeny, except when the organisms are under selection for high-frequency hearing.

How many exceptions we have in the fitting of the synonymous differences to the standard phylogeny?

Blas: The support of the theory of gravity do ot come from the explanations of the difference between the actual orbits and the ellipses but from the scientific experiments of gravity.

That's clearly wrong. It's called universal gravitation because it unifies the fall of the apple and the movements of the planets.

Blas: How many exceptions we have in the fitting of the synonymous differences to the standard phylogeny?

See Li et al., Echolocation is a sensory mechanism for locating, ranging and identifying objects which involves the emission of calls into the environment and listening to the echoes returning from objects [1]. Only microbats and toothed whales have acquired sophisticated echolocation, indispensable for their orientation and foraging [1]. Although the bat and whale biosonars originated independently and differ substantially in many aspects [2], we here report the surprising finding that the bottlenose dolphin, a toothed whale, is clustered with microbats in the gene tree constructed using protein sequences encoded by the hearing gene Prestin, Current Biology 2010.

Zachriel saidWhen it leads to a heritable change, it's called evolution.

Exactly, but we do not see actual heritable changes, adaptations changes like the changes in Darwin´s finches beaks goes for and back with changing environmental conditions. To make a dolphin with a pig you need more than what we see in the Galapagos.

Zachriel saidThat's clearly wrong. It's called universal gravitation because it unifies the fall of the apple and the movements of the planets.

No, calling “universal” gravitation is not scientific. We can only suppose that is universal hopping the dark matter exists. And that is not the point. The point is that the strong support for gravitation comes from de experiments we make here on earth not from the explanation of the disagreement for what we see in the space. Dark matter is not support for the “universal” gravitation is an hypothesis to keep gravitation universal.

Blas: Exactly, but we do not see actual heritable changes, adaptations changes like the changes in Darwin´s finches beaks goes for and back with changing environmental conditions.

While there is some oscillation, they never return to their previous condition. In either case, that's called natural selection.

Blas: To make a dolphin with a pig you need more than what we see in the Galapagos.

Pigs did not evolve into dolphins. They do share a common ancestor, though.

Blas: No, calling “universal” gravitation is not scientific.

You're saying Newton's Universal Law of Gravitation isn't scientific?

Blas: The point is that the strong support for gravitation comes from de experiments we make here on earth not from the explanation of the disagreement for what we see in the space.

That is simply false. The central notion of Newton's Theory of Gravitation is that the force of gravity affects both the moon and the apple, the motion of planets in their orbits, as well as the rate of falling of the apple.

No I´m saying that stating that that law is universal (valid at any place and any time of the Universe) is a not scientific claim. You do not have evidence for that. May be you have evidence on the contrary unless dark matter exists.

Zachriel saidThat is simply false. The central notion of Newton's Theory of Gravitation is that the force of gravity affects both the moon and the apple, the motion of planets in their orbits, as well as the rate of falling of the apple. .

And is strong supported because we can “explain” that the orbits of the planets are not perfect ellipses?

Excellent article. Decades of trying to align parts of genomes have not produced the hierarchical tree predicted by common ancestry, in spite of selective massaging the available data. A fresh conceptual start is needed, based on understanding the various codes involved and the informational outcomes deliberately Designed. Only then will facts such as lineage-specific mi-RNAs and cis-regulatory patterns start to make sense.